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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattataatgagcaataacggtaaaataaagagtcaactgatcagtacattccaaatctgtattgaatagtttgtaacttaggcttaatcttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA

Basic information

species Zea mays
transcript GRMZM2G131667_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131667_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g42250.2 (Oryza sativa), 3'ss of exon 4
gcattataatgagcaa-taacggtaaaataaagagtcaactgatcagta-cattccaaatctgtattgaatagtttgtaactt-aggcttaatcttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA
   | ||  ||  ||  ||    |      |  |  | | |||| |||  |||||   || | |||  ||   |   |||| | | || | ||   | |||||| ||||||||| |||| || ||||| |||||  ||||||||||||||||| |  | | ||| || || || |||||||||||| ||   ||||| |||||
--gtgatggtgttcatctagtttttcctggatcaccctagtgataagtctcattcttcatttctatgaaactatgcataacatgaagcctgatacct-ggcagGATGGACACATCTAGAGACCATTGACTCACTGATGAGGAAGGCAGGTTACAATGGTACCATAACCGACTCTTTGAGGAAGAAACTCCGTGTCACCCGCTA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37381281|gb|CF627515.1|CF627515
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|20208213|gb|BQ134302.1|BQ134302
EST:     CATCACAATACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|211365709|gb|FL031158.1|FL031158
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|91877199|gb|EB407156.1|EB407156
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|4776649|gb|AI665652.1|AI665652
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|5006220|gb|AI712282.1|AI712282
EST:     CAACNCAAAACCCAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|5439500|gb|AI820421.1|AI820421
EST:     TGCGGGCCATGAAG                         GNTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: TGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|21987668|gb|BQ779196.1|BQ779196
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|5455981|gb|AI833671.1|AI833671
EST:     GTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: GTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|30160506|gb|CB924235.1|CB924235
EST:     CAACACAAAACACAGTGCGACCTACTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|44900457|gb|CK827002.1|CK827002
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|60343398|gb|DN210371.1|DN210371
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|60351758|gb|DN218731.1|DN218731
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|5895985|gb|AW037231.1|AW037231
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
EST: gi|38229665|gb|CF919978.1|CF919978
EST:     CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAG                         GTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC
genomic: CAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 182

GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 286

GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 266

GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 428

GTTGGAAAGCATGGTTTAATTATTGAATTTACAGCTCCAGACTCCAACACAAAACACAGTGCGACCTATTTGCCTGAAGTTGCGGGCCATGAAGgtgaaaattt ... cttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacattccaaatctgtattgaatagtttgtaacttaggcttaatcttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA
                                            tctttt  CT-rich tract
                                        ttaatctttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattataatgagcaataacggtaaaataaagagtcaactgatcagtacattccaaatctgtattgaatagtttgtaacttaggcttaatcttttggcagGTTGGACACATGTAGAAACTATTGATTCACTCGTGAGGAAGGCAGGTTACCAGAGAATCATCACTGAGTCCTTGAGGAAGAAAATCAAAGTCACTCGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - cattcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattg